celldetective 1.0.2__py3-none-any.whl

celldetective/filters.py

@@ -0,0 +1,89 @@
+from skimage.filters import difference_of_gaussians, threshold_otsu, threshold_local, threshold_niblack, threshold_sauvola
+import scipy.ndimage as snd
+import numpy as np
+
+def gauss_filter(img, sigma, *kwargs):
+	return snd.gaussian_filter(img.astype(float), sigma, *kwargs)
+
+def median_filter(img, size, *kwargs):
+	size = int(size)
+	return snd.median_filter(img, size, *kwargs)
+
+def maximum_filter(img, size, *kwargs):
+	return snd.maximum_filter(img.astype(float), size, *kwargs)
+
+def minimum_filter(img, size, *kwargs):
+	return snd.minimum_filter(img.astype(float), size, *kwargs)
+
+def percentile_filter(img, percentile, size, *kwargs):
+	return snd.percentile_filter(img.astype(float), percentile, size, *kwargs)
+
+def subtract_filter(img, value, *kwargs):
+	return img.astype(float) - value
+
+def abs_filter(img, *kwargs):
+	return np.abs(img)
+
+def ln_filter(img, *kwargs):
+
+	img[np.where(img>0.)] = np.log(img[np.where(img>0.)])
+	img[np.where(img<=0.)] = 0.
+
+	return img
+
+def variance_filter(img, size):
+
+	size = int(size)
+	img = img.astype(float)
+	win_mean = snd.uniform_filter(img, (size,size))
+	win_sqr_mean = snd.uniform_filter(img**2, (size,size))
+	img = win_sqr_mean - win_mean**2
+
+	return img
+
+def std_filter(img, size):
+
+	size = int(size)
+	img = img.astype(float)
+	win_mean = snd.uniform_filter(img, (size,size))
+	win_sqr_mean = snd.uniform_filter(img**2, (size, size))
+	win_sqr_mean[win_sqr_mean!=win_sqr_mean] = 0.
+	win_sqr_mean[win_sqr_mean<=0.] = 0. # add this to prevent sqrt from breaking
+	img = np.sqrt(win_sqr_mean - win_mean**2)
+
+	return img
+
+def laplace_filter(img, output=float, *kwargs):
+	return snd.laplace(img.astype(float), *kwargs)
+
+def dog_filter(img, sigma_low, sigma_high, *kwargs):
+	return difference_of_gaussians(img.astype(float), sigma_low, sigma_high, *kwargs)
+
+def otsu_filter(img, *kwargs):
+	thresh = threshold_otsu(img.astype(float))
+	binary = img >= thresh
+	return binary.astype(float)
+
+def local_filter(img, *kwargs):
+	print(*kwargs)
+	thresh = threshold_local(img.astype(float), *kwargs)
+	binary = img >= thresh
+	return binary.astype(float)
+
+def niblack_filter(img, *kwargs):
+	thresh = threshold_niblack(img, *kwargs)
+	binary = img >= thresh
+	return binary.astype(float)
+
+def sauvola_filter(img, *kwargs):
+	thresh = threshold_sauvola(img, *kwargs)
+	binary = img >= thresh
+	return binary.astype(float)
+
+def log_filter(img, sigma, *kwargs):
+	return snd.gaussian_laplace(img.astype(float), sigma, *kwargs)
+
+def tophat_filter(img, size, connectivity=4, *kwargs):
+	structure = snd.generate_binary_structure(rank=2, connectivity=connectivity)
+	img = snd.white_tophat(img.astype(float), structure=structure, size=size, *kwargs)
+	return img

celldetective/gui/__init__.py

@@ -0,0 +1,20 @@
+from .styles import Styles
+from .btrack_options import ConfigTracking
+from .json_readers import ConfigEditor
+from .tableUI import TableUI
+from .measurement_options import ConfigMeasurements
+from .neighborhood_options import ConfigNeighborhoods
+from .classifier_widget import ClassifierWidget
+from .survival_ui import ConfigSurvival
+from .plot_signals_ui import ConfigSignalPlot
+from .signal_annotator_options import ConfigSignalAnnotator
+from .signal_annotator import SignalAnnotator
+from .retrain_signal_model_options import ConfigSignalModelTraining
+from .retrain_segmentation_model_options import ConfigSegmentationModelTraining
+from .thresholds_gui import ThresholdConfigWizard
+from .seg_model_loader import SegmentationModelLoader
+from .process_block import ProcessPanel, NeighPanel
+from .analyze_block import AnalysisPanel
+from .control_panel import ControlPanel
+from .configure_new_exp import ConfigNewExperiment
+

celldetective/gui/about.py

@@ -0,0 +1,44 @@
+from PyQt5.QtWidgets import QWidget, QVBoxLayout, QLabel
+from PyQt5.QtGui import QPixmap
+from PyQt5.QtCore import Qt
+from celldetective.utils import get_software_location
+import celldetective
+import os
+from celldetective.gui.gui_utils import center_window
+
+class AboutWidget(QWidget):
+
+	def __init__(self):
+
+		super().__init__()
+		self.setWindowTitle("About celldetective")
+		self.setMinimumWidth(300)
+		center_window(self)
+		logo = QPixmap(os.sep.join([get_software_location(),'celldetective','icons','logo.png']))
+
+		# Create the layout
+		layout = QVBoxLayout(self)
+		img_label = QLabel('')
+		img_label.setPixmap(logo)
+		layout.addWidget(img_label, alignment=Qt.AlignCenter)
+
+		self.soft_name = QLabel('celldetective')
+		self.soft_name.setStyleSheet("""font-weight: bold;
+										font-size: 18px;
+									""")
+		layout.addWidget(self.soft_name, alignment=Qt.AlignCenter)
+
+		self.version_lbl = QLabel(f"Version X.X.X <a href=\"https://github.com/remyeltorro/celldetective/releases\">(release notes)</a>")
+		self.version_lbl.setOpenExternalLinks(True)
+		layout.addWidget(self.version_lbl, alignment=Qt.AlignCenter)
+
+		self.lab_lbl = QLabel("Developed at Laboratoire Adhésion et Inflammation (LAI) INSERM U1067 CNRS UMR 7333")
+		self.lab_lbl.setWordWrap(True)
+		layout.addWidget(self.lab_lbl, alignment=Qt.AlignCenter)
+
+		self.centuri_mention = QLabel("The project leading to this publication has received funding from France 2030, the French Government program managed by the French National Research Agency (ANR-16-CONV-0001) and from Excellence Initiative of Aix-Marseille University - A*MIDEX')")
+		self.centuri_mention.setWordWrap(True)
+		layout.addWidget(self.centuri_mention, alignment=Qt.AlignCenter)
+
+
+